In situ detection of early stages and late stages HPV einfection

ABSTRACT

Embodiments of the invention provide methods, monoclonal antibodies, polyclonal antibodies, assays, and kits for detecting HPV infection and HPV related cancer diagnosis, including infection by various HPV genotypes, early and/or late stage HPV-associated or HPV-specific cancers. The anti-HPV antibodies are used in performing immunological assays on clinical samples. Various immunological assays and kits for detecting HPV infection, cervical cancer, other HPV related cancers, early stage precancerous lesions as well as late stage cancer progression are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims benefit of U.S. provisional patent application Ser. No. 61/131,991, filed Jun. 13, 2008, and U.S. provisional patent application Ser. No. 61/192,912, filed Sep. 22, 2008. Each of the aforementioned related patent applications is herein incorporated by reference.

BACKGROUND OF THE INVENTION

Infection by human papillomaviruses (HPV) at specific epithelium cells to induce epithelial proliferations plays an important role for cervical carcinogenesis. About 99 percent of confirmed cervical cancer cases are found to be associated with HPV infection with biopsy-confirmed squamous intraepithelial lesions (SIL) or cervical intraepithelial neoplasia (CIN). The incidence of HPV infection, primarily transmitted through sexual contact, is highest among young women and about 20 millions of sexually active men and women worldwide are currently infected. Approximately 1% of the population has genital warts and 4% of women have cervical precancerous lesions, such as low grade of squamous intraepithelial lesion (LSIL) or high grade of squamous intraepithelial lesion (HSIL) or atypical squamous cells of undetermined significance (ASCUS).

The presence of these lesions, preferentially observed in women aged 35-40 yrs, are at high risk of progression toward invasive cervical cancer. It is general thought that persistent infection of human papillomavirus (HPV) is essential for developing precancerous epitheliual lesions. Infection of high-risk types HPV for women with LSIL may or may not progress to HSIL. In fact, remission occurs in majority of LSIL human subjects while some progress to HSIL. Although 99.7% of cervical cancers are HPV positive, integration of viral genome into the host genome is required to facilitate the necessary genes to express for developing into HSIL or cancer. In fact, only one in every 10 women with persistent HPV infection may develop into higher grades of CIN lesions, such as cervical intraepithelial neoplasia (CIN) grade 2 and grade 3 (CIN2, and CIN3, respectively), and a portion of these epitheliual lesion cases may ultimately progress into cervical cancer.

In the past, screening for cervical cancer is based on conventional cytology screening tests, e.g., obtaining papanicolaou (Pap) smears for cytological staining tests, and suspicious smears are followed up with colposcopy, and/or histological biopsy. The use of these cytological screening tests contributes to a reduction in the mortality of cervical cancer. However, due to subjective test criteria, there are various drawbacks for pap smear tests: difficulty in obtaining samples, poor inter- and intra-observer agreement, high rates of false negatives nd false positives, requiring specialized labs staffed with highly trained personnel, and inability to identify the majority of HPV-infected human subjects. More reproducible assays are needed to improve the current screening tests to avoid unnecessary medical intervention and psychological distress for the affected women. The current conventional cervical cytology screening tests have sensitivity varied from about 30% to about 87%.

Detecting HPV infection by nucleic acid tests, such as “DNA Hybrid Capture”, has been developed with high assay sensitivity, but are still not ideal, due to not only its high cost, assay operation procedures, the requirements for facility, equipment, and highly trained personnel, but also its very low positive predictive value (PPV) in cervical intraepithelial neoplasia (CIN) testing samples. Assay like PreTect HPV-Proofer® provides the detection of E6/E7 mRNA with sensitivity equivalent to HPV Hybrid Capture tests with higher positive predictive value; but cannot directly detect E6/E7 oncoprtoeins in situ. In addition, DNA testing could not differentiate disease stages after HPV infection nor the diagnosis of different cell lesions (e.g., cannot diffrentiate LSIL from HSIL, nor CIN lesions from non-transforming latent or remissive viral infection). What is needed is a low cost, simple, sensitive and specific assay that can be performed on routine practice of a clinical lab or doctor office and capable of detecting early stages of epithelial lesions, distinguish LSIL from HSIL, or predicting the risk of progression into cervical cancer.

Known protocols for producing monoclonal antibodies are generally unsuitable for the production of anti-HPV monoclonal antibodies and cannot be used in immunocytochemical diagnostic tests performed on human subjects of general population. This is because antibodies produced by these protocols will not necessarily react with the naturally occurring HPV viral proteins in infected human cells. It is thought that the epitopes recognized by antibodies if generated by conventional protocols will not necessarily be those epitopes which are resistant to the harsh procedures involved in standard sampling, fixing and storing of clinical specimens. In addition, three problems exist in clinical HPV detection. One is that HPV proteins in clinical samples are present in very small quantities. Secondly, there are too many HPV types and most HPV types present in clinical samples are not known or systemically identified due to the lack of available antibodies. Third, HPV virus can not be cultured in labs by standard tissue culture techniques. Thus, there is no available HPV proteins purified to large quantities as immunogens for generating anti-HPV antibodies, and there is no available HPV proteins or purified anti-HPV antibodies to recognize anti-viral antibodies or viral proteins present in clinical samples for clinical HPV detection.

Infections by only about 15 HPV types (out of more than 100 available HPV types) are at high risk of developing into cervical intraepithelial neoplasia (CIN) or cervical cancer. Among them, around 70% of reported cervical cancer cases and 50% of reported CIN 2 and CIN 3 cases are caused by two high risk HPV types, i.e., HPV type-16 and HPV type-18. However, some progressive cervical cancer cases are reported to be infected by low risk HPV types, while infection of some high risk HPV types will never progress into cervical cancer. Infections by these two prevailing high risk HPV types do not correlate with tumor development or cancer progression. It seems important to identify those HPV-infected human subjects that express particular oncogenic proteins rather than just identify HPV infection by high risk types.

Thus, there is a need for detect the expression of HPV-related oncoproteins in clinical samples as these oncoprotiens may better serve as cervical cancer biomarkers to better predict the risk in developing into high grade of cell lesions or cervical cancer-related diseases. There is also a need to develop anti-HPV antibodies and appropriate HPV immunoassays to detect the presence of invasive cervical cancer and/or HPV-related oncoproteins as cervical cancer biomarkers and predict the risk for malignant transformation of epithelial lesions into cervical cancer.

SUMMARY OF THE INVENTION

Embodiments of the invention provide various immunoassays for in situ detection of HPV proteins using various monoclonal antibodies against recombinant HPV proteins such that infection by high risk and/or low risk HPV types can be detected by a single specific monoclonal antibody and/or a general pan antibody. The invention also provides HPV immunocytochemistry (ICC) assay, HPV flow cytometry assay, HPV immunohistochmistry (IHC) assay to detect the presence of HPV proteins in cervical cells or cervical tissues. In addition, monoclonal antibodies highly specific for HPV viral proteins are also provided to be used in the HPV ICC or HPV flow cytometry assays.

In one embodiment, a method of detecting papillomavirus infection in a human subject is conducted by an immunocytological assay to detect in situ one or more papillomavirus proteins from one or more papillomavirus types present in a biological sample on a slide containing a thin layer of human cells, using one or more antibodies to stain the thin layer of human cells. The method includes providing a clinical sample from the human subject, the clinical sample is processed into a mixture of morphologically abnormal and normal human cells, applying the mixture into a thin layer of cells on a slide, and conducting an immunocytochemistry assay using one or more antibodies generated against one or more purified recombinant papillomavirus proteins, such that one or more papillomavirus viral proteins from one or more papillomavirus types present in the clinical sample on the slide containing the mixture of morphologically abnormal and normal human cells is stained in situ.

In another embodiment, a method of detecting papillomavirus infection in a human subject includes providing a clinical sample from the human subject and tagging one or more antibodies with an agent, wherein the clinical sample is processed into a liquid-based solution containing a mixture of morphologically abnormal and normal human cells. The mixture of the morphologically abnormal and normal human cells is stained using the one or more antibodies generated against one or more purified recombinant papillomavirus proteins. The method further includes conducting one or more flow cytometry assays to detect each individual cells by separating each cell from the mixture of the morphologically abnormal and normal human cells, and detecting the presence of one or more human papillomavirus viral proteins from one or more papillomavirus types in the mixture of the morphologically abnormal and normal human cells contained in the liquid-based solution from the clinical sample.

In one embodiment, the one or more antibodies are generated against one or more purified recombinant papillomavirus proteins, wherein at least one antibody is capable of recognizing a papillomavirus early protein. In another embodiment, the one or more antibodies are tagged with an agent, and one or more human cells from a biological sample of the human subject are prepared into a liquid-based solution, such that the binding of the one or more antibodies with the one or more papillomavirus proteins from one or more papillomavirus types present in the one or more human cells of the biological sample can be detected by the presence of the agent reacting with the tagged one or more antibodies. In another embodiment, the agent includes a colormetric agent, a fluorescent chromogen, and other agent for later separation and identification of the one or more human cells in one or more flow cytometry assays.

In addition, a kit for performing an immunocytological assay is provided. The kit may include an pre-antibody blocking solution, post-antibody blocking solution, an anti-HPV antibody as the primary antibody, an anti-mouse or anti-rabbit immunoglobulins conjugated with HRP or biotin, or other agents as secondary antibody, a solution containing appropriate agents used as substrate for the secondary antibody to be detected.

In still another embodiment, a kit is provided for detecting papillomavirus infection in a human subject and includes an anti-HPV monoclonal antibody capable of binding to a papillomavirus early protein for conducting an immunocytochemistry assay on a clinical sample from the human subject processed into a solution containing a mixture of morphologically abnormal and normal human cells and applied into a thin layer of cells on a slide for staining in situ one or more papillomavirus viral proteins from one or more papillomavirus types present in the clinical sample on the slide containing the mixture of morphologically abnormal and normal human cells.

SUMMARY OF DRAWING

FIG. 1A shows the staining results of a clinical sample, diagnosed as ASCUS, in a liquid based solution using an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to one embodiment of the invention.

FIG. 1B shows the staining results of the same clinical sample as shown in FIG. 1A using an anti-HPV E7 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 2A shows the staining results of a clinical sample, diagnosed as CIN2, in a liquid based solution using an anti-HPV E7 mouse monoclonal antibody in an ICC assay according to one embodiment of the invention.

FIG. 2B shows the staining results of another clinical sample, diagnosed as CIN2, in a liquid based solution using an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 3A shows the staining results of a clinical sample, diagnosed as CIN3, in a liquid based solution using an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 3B shows the staining results of another clinical sample, also diagnosed as CIN3, and stained with the same anti-HPV E6 mouse monoclonal antibody as the one used in FIG. 3A.

FIG. 3C shows another ICC staining image on the same clinical sample as used in FIG. 3B and stained with the same anti-HPV E6 mouse monoclonal antibody.

FIG. 3D shows another ICC staining image on the same clinical sample as used in FIG. 3B and stained with the same anti-HPV E6 mouse monoclonal antibody.

FIG. 3E shows another ICC staining results on the same CIN3 sample as used in FIG. 3B but stained with an anti-HPV E7 mouse monoclonal antibody according to another embodiment of the invention.

FIG. 3F shows another ICC staining image of the same CIN3 sample as shown in FIG. 3E and stained with the same anti-HPV E7 mouse monoclonal antibody.

FIG. 3G shows the staining results on the same CIN3 sample as shown in FIG. 3B but stained with an anti-p16 mouse monoclonal antibody in an ICC assay.

FIG. 4 shows the staining results of a clinical sample diagnosed as adenocarcinoma and stained with an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 5A shows the staining results of a clinical sample diagnosed as squamous cell carcinoma (SCC) and stained with an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 5B shows the staining results of the same SCC sample as used in FIG. 5A and stained with an anti-HPV E7 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 5C shows the staining results of the same SCC sample as shown in FIG. 5A using an anti-p16 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 6A shows the staining results of a clinical sample diagnosed as normal and stained with an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 6B shows the staining results of the same clinical sample as shown in FIG. 6A and stained with an anti-HPV E7 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 7A shows staining of the cytoplasmic portions of another cervical scrape sample with an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 7B shows staining of the nuclear portions of the same sample as used in FIG. 7A with an anti-HPV E7 mouse monoclonal antibody.

FIG. 7C shows staining of the cytoplasmic portions of another cervical scrape sample with an anti-HPV E6 mouse monoclonal antibody.

FIG. 8A shows the staining results of a clinical sample diagnosed as CIN1 and stained with an anti-HPV E6 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 8B shows another ICC staining image of the same CNI1 sample as shown in FIG. 8A using the same anti-HPV E6 mouse monoclonal antibody.

FIG. 8C shows another ICC staining image of the same CIN1 sample as shown in FIG. 8A using the same anti-HPV E6 mouse monoclonal antibody.

FIG. 8D shows the staining results of the same CIN1 sample as shown in FIG. 8A but stained with an anti-HPV E7 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

FIG. 8E shows another ICC staining image of the same CIN1 sample as shown in FIG. 8D stained with the same anti-HPV E7 mouse monoclonal antibody.

FIG. 8F shows the staining results of the same CIN1 sample as shown in FIG. 8A using an anti-p16 mouse monoclonal antibody in an ICC assay according to another embodiment of the invention.

DETAILED DESCRIPTION

Embodiments of the invention provide various immunoassays and monoclonal antibodies against HPV viral proteins such that infection by high risk and low risk HPV types can be detected by a single monoclonal antibody and/or a general pan antibody. The invention also provides HPV immunocytochemistry (ICC) assay, HPV flow cytometry assay, HPV immunohistochmistry (IHC) assay to detect the presence of HPV proteins in situ.

A method for detecting papillomavirus infection in a human subject includes conducting one or more immunological assays, such as an immunocytological assay, a flow cytometry assay on a clinical sample from the human subject and processed into a mixture of morphologically abnormal and normal human cells. In one embodiment, an immunocytological assay is conducted by processing the mixture of human cells into a thin layer of human cells on a slide. The thin layer of human cells can be, for example, a monolayer of cervical cells. The mixture of human cells can be applied to the slide by direct smear or from a liquid based solution. The one or more papillomavirus proteins from one or more papillomavirus types present in the clinical sample is then detected in situ by staining the thin layer of human cells with one or more tagged antibodies generated against one or more purified recombinant papillomavirus proteins. The one or more antibodies can be tagged with different agents suitable in the art for visualization, such as stainins agents or detection agents. In one embodiment, at least one antibody of the one or more antibodies is capable of recognizing a papillomavirus early protein. The papillomavirus early protein may be, for example, HPV-16 E6 protein, HPV-16 E7 protein, HPV-18 E6 protein, HPV-18 E7 protein, and combinations thereof.

Another method of detecting papillomavirus infection in a human subject includes conducting a flow cytometry assay on human cells from biological samples obtained from a human subject and provided in a liquid-based solution to detect one or more papillomavirus proteins from one or more papillomavirus types present in the samples. The flow cytometry assay can be conducted to detect each individual cell by separating the one or more human cells in accordance with, e.g., cell size, staining with agents tagged on one or more antibodies, or other criteria. In addition, the presence of one or more proteins from one or more papillomavirus types in the human cells contained in the liquid-based solution of the biological sample is detected by one or more tagged antibodies. The one or more flow cytometry assays is conducted by a group of flow cytometry instruments with capability to separate and detect each cell individually in a flow format using appropriate light source for detection.

In another embodiment, one or more immunohistochemical assays on the slide containing the thin section of the clinical tissue sample; was conducted to stain the human cells using one or more antibodies generated against one or more purified recombinant papillomavirus proteins, wherein at least one antibody is capable of recognizing a papillomavirus early protein; and detecting in situ one or more proteins from one or more papillomavirus types present in the thin section of the clinical tissue sample on the slide.

In another embodiment, cytological papanicolaou smear assay on the clinical sample was also performed to compare the results of the cytological papanicolaou smear assay with the results of the one or more immunohistological assays. Nucleic acid hybridization assay on the clinical sample was also performed to detect the presence of a papillomavirus genome in the clinical sample from the human subject

Embodiments of the invention generally relate to various methods, detection assays, kits, polyclonal and monoclonal antibodies, polypeptides, recombinant proteins, and nucleic acids useful for detecting HPV infection, including general HPV infection as well as infection by various HPV genotypes, high risk HPVs and low risk HPVs. Various novel monoclonal antibodies against HPV proteins, useful as biomarkers and useful tools for detecting HPV viral proteins, HPV oncoproteins, early screening of cervical cancer, and diagnosing CIN and/or invasive cervical and other cancers, are provided. The tools of the inventions can also be used in early clinical screening for HPV infection and general diagnosis for cervical cancer and other cancers, specific detection of invasive cervical cancer, detection of other HPV related cancers, early stage precancerous lesions as well as late stage cancer progression.

In another embodiment, the one or more purified recombinant papillomavirus proteins include recombinant E6 proteins, recombinant E7 proteins, recombinant L1 proteins from various HPV types. The recombinant papillomavirus proteins include, but not limited to recombinant HPV-16 E6 proteins, recombinant HPV-16 E7 proteins, recombinant HPV-18 E6 proteins, recombinant HPV-18 E7 proteins, recombinant HPV-16 L1 proteins, recombinant HPV-18 L1 proteins combinations thereof. One of embodiment provides various monoclonal antibodies against HPV viral proteins such that infection by high risk and low risk HPV types can be detected by a single monoclonal antibody. The invention also provides HPV type specific monoclonal antibodies for detecting only the high risk HPV types. The one or more papillomavirus types includes high risk HPV types, low risk HPV types, HPV-16, HPV-18, HPV-31, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51, HPV-52, HPV-56, HPV-58, HPV-59, and HPV-68, HPV-6, HPV-11, HPV-42, HPV-43, HPV-44, HPV-53, HPV-54, HPV-55, and HPV-56, and combinations thereof.

In one embodiment, one antibody among the one or more antibodies is capable of recognizing a common epitope present on two or more papillomavirus proteins. The two or more papillomavirus proteins may include a papillomavirus early protein and a late papillomavirus protein and the one antibody is capable of recognizing both the papillomavirus early protein and the late papillomavirus protein. In another embodiment, the one or more antibodies may include antibodies recognizing HPV E6 proteins, antibodies recognizing HPV E7 proteins, antibodies recognizing both HPV E6 and E7 proteins, antibodies recognizing HPV L1 proteins, antibodies recognizing HPV E6 proteins from different HPV types, antibodies recognizing HPV E7 proteins from different HPV types, antibodies recognizing HPV L1 proteins from different HPV types, antibodies recognizing HPV E6 and E7 proteins of the same HPV types, antibodies recognizing HPV E6 and E7 proteins of different HPV types, antibodies recognizing HPV E6, E7, and L1 proteins, and combinations thereof.

The binding of the antibody with the one or more HPV viral proteins from one or more papillomavirus types present in the biological sample are examined under a microscope to detect the presence of an agent reacting with the tagged one or more antibodies, wherein the agent consists of a colormetric agent, a fluorescent chromogen, and combinations thereof. The biological sample consists of cervical cells, cervical tissues, cervical swabs, body fluids, serum, blood, tumors, cell cultures, biopsies, and combination thereof. The biological sample can be obtained from a group of people as general population for routine screening of cervical cancer.

As an example, a mouse anti-HPV E6 or anti-HPV E7 monoclonal antibody can be used in an ICC assay in a liquid based solution to detect the presence of HPV E6 or HPV E7 protein in situ on one or more cells fixed on a slide. The liquid based solution can be various liquid based solutions useful for the ICC assay. Using the methods, antibodies, and assays of the invention, HPV E6 or HPV E7 proteins can be detected in situ on cervical scrape samples of a general population with HPV infection at various disease stages. In one embodiment, the immunocytological assay is used to a diseased stage caused by HPV infection. The disease stage may be early stage HPV infection, late stage HPV infection, early stage cervical cell lesion, late stage cervical cell lesion, low grade of squamous Intraepithelial lesion (LSIL), high grade of squamous intraepithelial lesion (HSIL). atypical squamous cells of undetermined significance (ASCUS), cervical intraneoplasm stages 1, 2, 3 (CIN1, CIN2, CIN3, respectively), developed cervical cancer, or adenocarcinoma, squamous cell carcinoma (SCC). In addition, the same cervical scrape samples can also be processed by standard cytological papanicolaou smear assays to compare the results of the cytological papanicolaou smear assay with the results of the immunocytological assays. Further, the staining pattern and intensities of the mixture of the morphologically abnormal and normal human cells as performed in accordance with the methods and assays of the invention can be compared with the morphology of these human cells.

As another example, immunological assays are performed on cervical scrape samples diagnosed as normal, ASCUS, ASC-H, CIN1, CIN2/3, and HPV E6 viral proteins are detected to be present in these samples with increasing positivity rate, respectively, using an anti-HPV E6 antibody. There is about 92% positive rate for samples diagnosed with pap smear CIN2/3, while only 15% of samples diagnosed as pap smear normal is stained positively in an ICC assay using the anti-HPVE6 antibody. For ASCUS or ASC-H samples, about 33% to 38% of these samples are stained positively by the same anti-HPV E6 antibody as used for the CIN2/3 samples, indicating HPV infection and the expression of oncogenic proteins in these ASCUS or ASC-H samples. Thus, the results from the immunological assays of the invention help to identify the need for these ASCUS or ASC-H human subjects to come back to a medical clinic for follow-up testing of potential cancer development and disease progression. For the ASCUS and ICC clinical samples that are tested negative by the anti-HPV E6 antibody in n ICC assay, it can be predicted that there is less risk to develop progressive HPV-related cervical lesions. Accordingly, the results the ICC staining assay using the anti-HPV E6 antibody assay sensitivity of 83% for CIN2+ with specificity of 85%. These data suggest this assay can be useful to detect HPV proteins for screening of cervical cancer from general population along with routine pap smear staining. Similar ICC results were also found in the same samples using anti-HPV E7 antibodies.

In a further embodiment, nucleic acid hybridization assay can also be performed on the clinical sample to detect the presence of a papillomavirus genome in the clinical sample from the human subject. The nucleic acid hybridization assays consist of polymerase chain reactions, nucleic acid hybridization assays, DNA chip assays, radioactive nucleic acid hybridization and detection assays, and non-radioactive nucleic acid hybridization and detection assays.

In another embodiment, one or more flow cytometry assays was conducted to detect each individual cells by separating the one or more human cells with or without staining, and detecting the presence of one or more proteins from one or more papillomavirus types in the one or more human cells contained in the liquid-based solution of the biological sample. The one or more flow cytometry assays is conducted by a group of flow cytometry instruments consisting of capability to separate and detect each cell individually in a flow format using appropriate light source for detection.

As an example, cells from cervical scrapes were collected, centrifuged, washed, and immunostained followed by the ICC procedure described herein. The HPV E6, E7, or L1 protein can be detected by the specific antibody followed by the 2^(nd) antibody labeled with fluorescent dye (FITC, PE, Cy5, etc. conjugated). The cells analyzed by flow cytometry can be gated by size or other parameter to look at the cell population with or without staining. The stain intensity from cell population with smaller cell size can be compared to the cell population with bigger cell size as control of normal cells in the assay. This assay provides specific staining for individual cells. Number of cells stained or unstained can be counted, and the intensity of staining can also be quantitated by analysis. This assay can be high throughput, requires no microscope, nor cytologist to score the staining results. The powerful computer software from the flow cytometry provides all data for analysis with no bias nor trained personel in cytology required. This assay should apply well in the clinical setting as screening test or accompanion test for detection of HPV associated proteins.

In another embodiment, one or more immunohistochemical assays on the slide containing the thin section of the clinical tissue sample was conducted to stain the thin layer of human cells using one or more antibodies generated against one or more purified recombinant papillomavirus proteins, wherein at least one antibody is capable of recognizing a papillomavirus early protein; and detecting in situ one or more proteins from one or more papillomavirus types present in the thin section of the clinical tissue sample on the slide. cytological papanicolaou smear assay on the clinical sample and comparing the results of the cytological papanicolaou smear assay with the results of the one or more immunohistological assays.

For example, a number of cervical biopsy samples are tested in an immunohistohistochemistry (IHC) assay concurrently as a tissue microarray format using a monoclonal antibody to detect HPV proteins from a variety of HPV types (as confirmed by HPV DNA genotyping). Using a monoclonal antibody against HPV oncoprotein E7, the invention provides detection of the presence of HPV E7 protein in clinical samples having either single HPV infection or multiple HPV infections. A single anti-E7 monoclonal antibody as described herein can detect single HPV infection by at least HPV-6, HPV-16, HPV-18, HPV-31, HPV-33, HPV-52, etc, which are cancer-related HPV types (either high risk HPV types or low risk HPV types). A single anti-E7 monoclonal antibody can detect HPV infection by two or more HPV types, such as the combination of HPV-16, HPV-18, HPV-52, HPV-58, HPV-44, HPV-51, HPV-39, HPV-59, etc., which include high risk, low risk, and non-oncogenic α-papillomaviruses.

Two problems existed such that there is no antibody available to do clinical HPV diagnostics. One is that HPV proteins in clinical sample are present in very small quantities. Secondly, the HPV types in the clinical sample are generally unknown. Therefore, people skilled in the art failed and were not able to produce large scale production of HPV antibodies that recognizes various clinical HPV types, despite this long felt need, and the need is not solved. For successful use of an antibody in a diagnostic test the antibody must recognize an epitope which is present on the immunogen and the epitope can be exposed in the test sample being prepared for analysis (i.e., exposed after any pre-treatment of tissues such as cryopreservation, sectioning and fixing). Therefore, the method chosen for screening large numbers of hybridoma culture supernatants must be such that it aids selection of diagnostically useful antibodies. There has been known failure in purifying and obtaining recombinant HPV proteins and in producing antibodies from purified recombinant proteins for screening HPV infection and people have not been able to solve the need.

Accordingly, one embodiment of the invention provides a monoclonal antibody capable of recognizing a common epitope on E6 protein from two different HPV types, both HPV16 and HPV18 by screening antibody-producing hybridoma cells with a purified HPV16 E6 recombinant protein and a purified HPV18 E6 recombinant protein. Another embodiment of the invention provides a monoclonal antibody that recognizes a common epitope on HPV16 E7 and HPV18 E7 proteins. Still another embodiment of the invention provides a monoclonal antibody that recognizes a common epitope on HPV16 E6, HPV16 E7, HPV16 L1, HPV18 E6, and HPV18 E7 proteins.

In still another embodiment, a monoclonal antibody capable of recognizing a specific epitope on only one HPV viral protein, but not another HPV viral protein is obtained by screening antibody-producing hybridoma cells with a first purified recombinant papillomavirus protein from a first HPV type and a second purified recombinant papillomavirus protein from a second HPV type, wherein the one and another viral proteins correspond to the first and the second purified recombinant papillomavirus proteins of the first and second HPV types.

In another embodiment, various monoclonal antibodies against HPV proteins, E6, E7 or L1 (anti-HPV E6, anti HPV E7, anti-HPV-L1) are provided including those monoclonal antibodies specific for detecting HPV types correlated with the immunogens that the antibodies were raised, and other non-HPV type-specific monoclonal antibodies. The antibodies of the invention includes, but are not limited to anti-E6, anti-E7, and anti-L1 antibodies, etc., and are used in one or more immunological assays. For examples, the monoclonal antibodies can be used to test on various biological samples, cell lines, and/or clinical samples of various grades of epithelial lesions (CIN2, CIN3, LSIL, HSIL, ASCUS) as well as different cervical cancers, squamascarcinoma (SCC, a type of common cancer) and adenocarcinoma (ADC, a type of gland cancer).

In one embodiment, a method of screening a human subject of papillomavirus infection includes obtaining a clinical sample from the human subject, and conducting one or more immunological assays on the clinical sample from the human subject using various HPV recombinant proteins and lab-generated antibodies specific for HPV oncoproteins in order to detect and screen for the presence of HPV infection from the presence of HPV proteins and HPV antibodies in the human subject. In another embodiment, the HPV proteins in the human subject are detected using antibodies raised against HPV recombinant proteins, including but not limiting to various polyclonal and monoclonal antibodies against various HPV early and late proteins.

The antibodies as developed herein lend themselves to the high quality and properly purified recombinant proteins encoded by HPV early and late genes, useful in immunological assays with to generate very high sensitivity and specificity for screening HPV infection and cervical cancer detection. The monoclonal antibody can be used for one or more immunological assays selected from the group consisting of ELISA (enzyme linked imunoabsorbant assays), antigen assays for papillomavirus proteins, antibody assays for antibodies against papillomavirus proteins, assays for papillomavirus immunocomplexes, protein chip assays, radioimmunoprecipitation assays, rapid membrane immunochromatographic assays, rapid stick immunochromatographic assays, immunohistochmistry for tissues and/or cervical cells, and immunocytological assays followed by flow cytolmetry, among others. In one embodiment, the one or more immunological assays may be non-invasive with minimal or no additional instrument required.

The basic techniques for conducting the immunological assays can be found in “Antibodies: A Laboratory Manual”, Harlow and Lane, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 1989; “Molecular Cloning”, A Laboratory Manual, eds. Sambrook, Fritsch and Maniatis, Cold Spring Harbor Laboratory Press, 1989, and others books and manuals known in the art. The related immunological assays, immunohistochmistry for tissues and/or cervical cells, and/or immunocytological assays followed by flow cytolmetry can also be found in co-pending U.S. patent applications: Ser. No. 11/559,366, filed on Nov. 13, 2006, titled “Detection method for human pappilomavirus (HPV) and its application in cervical cancer”; Ser. No. 12/082,740, filed Apr. 14, 2008, titled “Protein chips for HPV detection”; Ser. No. 61/131,991, filed Jun. 13, 2008 titled “Antibodies and assays for HPV detection”; Ser. No. 61/192,912 Filed on Sep. 22, 2008, titled “Novel monoclonal antibodies against HPV proteins useful for early stage and late stage detection, screening, and diagnosis of HPV related cervical cancer”; Ser. No. ______ (NEOD/0004), filed concurrently as this application, titled “Novel monoclonal antibodies against HPVproteins”; Ser. No. ______ (NEOD/0005.02), filed concurrently as this application, titled “in situ detection of early stages and late stages HPV infection”; Ser. No. ______ (NEOD/0005.03), filed concurrently as this application, titled “Detection of early stages and alte stages HPV infection”. All of the above referenced applications are herein incorporated by reference.

In one embodiment, the invention also provides various methods, detection assays, and kits, polyclonal and monoclonal antibodies, polypeptides, recombinant proteins, and nucleic acids useful for detecting general HPV infection as well as infection by various HPV genotypes, high risk HPVs and low risk HPVs. In addition, the assays or sample formats in detecting the presence of HPV proteins are not limited and can be used for cervical tissues, cervical cells, cervical scrapes, serum, body fluids, etc. The useful screening or diagnosing assay can be IHC, ICC, flow cytometry, antibodies coupled to beads, rapid tests, protein chips, dot blots, slots, as well a conventional ELISA assay. HPV proteins can be detected by the antibodies of the invention to be present in epithelium tissue as evidenced by IHC staining after scoring by a pathologist.

The antibodies described in this invention provide a tool to detect HPV proteins present in various sources of biological samples. As an example, the antibodies described herein can be used as capture antibody to coat on microtiterplate and/or used as detection antibody as a sandwich format of ELISA (Enzyme Linked Immuno Sandwich Assay). Depending on detection of HPV proteins and/or HPV types, antibodies can be selected to use based on the specificity described herein of monoclonal antibody to particular HPV proteins or HPV types, or in combinations thereof. The detection antibody from selected specificity of monoclonal antibodies described herein can be directly conjugated with label like biotin, alkalin phosphatase, HRP, flourecent, etc., followed by color metric, chemiluminescent or fluorescent substrate for readout. The detection antibody can also select from polyclonal antibody described herein followed by a secondary antibody conjugated with label like biotin, alkalin phosphatase, HRP, flourecent, etc. Combination of using polyclonal and monoclonal antibodies for the sandwich ELISA as capture and detection antibody or vice versa, increases assay sensitivity by incorporating secondary antibody to amplify the signal for detection. For direct EIA (Enzyme Immuno Assay), cells, samples or cultured cells to be tested were collected and lysed to generate cell late as anyalyte. The protein in the cell lysate was quantitated and coated to microtiterplate using the same amount of protein for coating of each sample in each well followed by the detection antibody with specificity described in this invention.

Detection of HPV DNAs, genomes, early viral proteins, late viral proteins, oncoproteins, and/or capsid proteins from various HPV genotypes can be performed by various in vitro and in vivo method and detection assays according to “Antibodies: A Laboratory Manual”, Harlow and Lane, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. 1989; “Molecular Cloning”, A Laboratory Manual, eds. Sambrook, Fritsch and Maniatis, Cold Spring Harbor Laboratory Press, 1989, and others books and manuals and can be very useful in general clinical screening for HPV infection.

Detection of HPV antibodies and/or oncoproteins by immunological assays can be used in early clinical screening for HPV infection and general diagnosis for cervical cancer and can be performed in a single rapid test or in multiplexed test. Comparative detection of altered levels of HPV proteins and host proteins can be performed in the same or different assays. It can also be used in diagnosing HPV-associated carcinomas of the uterine cervix, as well as those cases associated with epithelial cell abnormalities induced by HPV infection, pre-malignant and malignant HPV-associated epithelial cell lesions, and those at risk of developing HPV-associated cervical carcinoma and adenocarcinoma. The methods as described herein can be used independently or as an adjunct screening tool to convention cytological papanicolaou smear tests or histological tests and the results thereof can be compared for follow-up patient management.

EXAMPLES

1. Expression, Purification, and Preparation of HPV Recombinant Proteins to be Used as Immunogens for Generating Antiserum and Anti-HPV Antibodies, and Screening Hybridoma Cell Lines for Monoclonal Antibodies

HPV recombinant proteins can be any kinds of HPV proteins, HPV proteins of early genes and/or late genes, including, but not limited to, E2, E6, E7, L1, L2 and can be from various HPV types. Full-length E6, E7, and/or L1 polypeptide sequence, which have been found very difficult to obtain and purify due to undesirable aggregation during protein purification, protein instability, low levels of expression, low immunogenic responses of purified proteins. For example, many early E6 oncoproteins contain many cysteine amino acids and thus the correct topography of the E6 oncoproteins requires formation of many disulfide bonds properly. In addition, it was known that certain immunological assays using small peptides of early E6 and E7 proteins results in extremely low assay specificity and sensitivity and thus unsuitable as tools for clinical in vitro diagnostics. Thus, the invention provides recombinant proteins, such as recombinant hybrid proteins containing a partial sequence or a full length sequence of HPV oncogenic proteins.

1). Cloning and production of various recombinant proteins encoded by HPV16 E6 and HPV18 E6 gene. An exemplary oncogenic E6 early gene from an exemplary HPV type, HPV-16, was clone. The HPV 16 E6 gene cloned herein is a 474 base pair (b.p.) DNA fragment containing the 157 amino acid coding region of the whole HPV-16 E6 gene and obtained by polymerase chain reaction (PCR) amplification. The DNA sequence of the isolated DNA fragment was confirmed by comparing with the sequence from Gene Bank database. Recombinant HPV-18 E6 protein was also obtained. All cloning procedures are carried out according to the protocols described in “Molecular Cloning”, A Laboratory Manual, eds. Sambrook, Fritsch and Maniatis, Cold Spring Harbor Laboratory Press, 1989. In addition, HPV18 E6 gene was also cloned and the DNA sequence was confirmed.

2). Cloning and production of various recombinant proteins encoded by HPV16 E7 and HPV18 E7 gene. An exemplary oncogenic E7 early gene from an exemplary HPV type, HPV-16, was cloned. A 294 base pair (b.p.) DNA fragment containing the 99 amino acid coding region of the entire HPV-16 E7 gene was obtained by polymerase chain reaction (PCR) amplification. The DNA sequence of the isolated DNA fragment was confirmed by comparing with the sequence from Gene Bank database. Recombinant HPV-18 E7 protein was also obtained In addition, E7 DNA fragments from different HPV types can also be cloned from different clinical samples or sources.

3). Cloning and production of various recombinant proteins encoded by HPV16 L1 and HPV18 L1 gene. An exemplary late gene from an exemplary HPV type, HPV-16, was cloned. A 1596 base pair (b.p.) DNA fragment containing the 531 amino acid coding region of the HPV-16 L1 gene was obtained by polymerase chain reaction (PCR) amplification. The DNA sequence of the isolated DNA fragment was confirmed by comparing with the sequence from Gene Bank database. In addition, L1 DNA fragments from different HPV types can also be cloned from different clinical samples or sources.

A recombinant N-terminal fragment of HPV 16 L1 protein was also obtained from a His-tagged expression system. The molecular weight of the HPV-16 L1 N-terminal recombinant protein is about 34 KD. L1 C-terminal fragments can also be obtained. Recombinant HPV-18 L1 protein was also obtained and used as immunogens for generating antiserum, polyclonal and monoclonal antibodies.

The one or more recombinant proteins as described herein can be expressed in various suitable systems, such as bacterial expression systems, viral expression systems, yeast expression systems, mammalian expression systems, e.g., in E coli, yeast, baculovirus, and/or mammalian cell cultures, generally known in the field. Although the polypeptides could be obtained by other means, embodiments of the invention provide one or more recombinant proteins mostly in (or close to) their native forms, which may be a much desirable conformation for binding with antibodies from tissues of human subjects with HPV infection in an immunological assay. For example, GST, MBP, or His tagged-HPV16-E6, HPV18 E6, HPV16 E7, HPV18 E7, HPV16 L1, and HPV18 L1 recombinant proteins were expressed in E. coli BL21(DE3) using IPTG driven induction. After induction of protein expression, tagged-HPV recombinant proteins were obtained from soluble fraction after lysis of the cultured cells and purified to a final concentration of about 0.1 to 1 mg/ml or higher. The purity of the recombinant HPV proteins was estimated to be >90% based on PAGE analysis. Recombinant HPV proteins were used to detect the presence of HPV antibody on clinical samples and was also used as immunogens for producing polyclonal antiserum and monoclonal antibodies.

The cell culture containing various recombinant papillomavirus proteins in various expression vectors as described herein are then scaled up to 1 liter or 10 liter, or 100 liters or higher to obtain high quantity of soluble recombinant protein for purification. The soluble fraction after cell lysis was passed through various chromatography columns with appropriate expression systems to bind to the tag expressed along with the HPV recombinant proteins. The tag-HPV recombinant proteins were then eluted from the column and concentrated down to 100 ml or 10 ml to 1 ml. The purified soluble recombinant HPV proteins were further concentrated and dailysed with buffers at neutral pH or PBS buffers to be used as immunogen to generate antiserum against the HPV proteins. The soluble recombinant HPV proteins were thus purified from soluble fractions and folded close to their native folding states as in vivo natural conditions.

Obtaining high quality purified recombinant HPV proteins is critical in generating various types of monoclonal antibodies that recognizing common epitopes or specific epitopes for detecting HPV infection. The purified recombinant HPV proteins were tested to confirm its binding to the HPV antibody from the HPV infected clinical samples. Thus, such purified recombinant HPV proteins are suitable for use as immunogen to raise antiserum and generate antibodies that can recognize natural HPV viral proteins in vivo.

2. Anti-HPV Polyclonal Antibody Production:

Recombinant HPV E6, E7 or L1 proteins expressed in E coli was purified, concentrated, and dialyzed with PBS to be used as immunogens. Immunization was followed by standard protocol. Titer of each serum obtained was tested by ELISA assays followed by periodical boosting and bleeding. Production bleed from optimal titer was collected; processed serum was used to do immunoglobulin (Ig) purification via protein A columns or affinity columns. Purified IgG was used as anti-HPV antibodies for HPV immunoassays.

Monoclonal antibodies, polyclonal antibodies, and antiserum were obtained, purified, and tested herein to be able to detect HPV infection regardless of the pathogenesis of HPV infection, cell lesions, inflammatory, or cancer disease development. Other researchers have tried to develop anti-HPV monoclonal antibodies but have failed because they failed to generate sufficient HPV proteins for monoclonal antibodies production; they failed to generate monoclonal antibodies with high specificity because the immunigens were not immunogenic; or the generated antibodies were not able to recognize native forms of HPV proteins present in clinical samples with early stage HPV infection. Some antibodies raised against mutant peptides were only able to recognize late stage cervical cancer, but are not sure whether their antibodies would recognize wild type HPV native proteins or any early stage HPV infection. In addition, late stage HPV detection is too late for disease intervention and treatment.

The clinical utility of the antibodies described herein was validated by HPV immunoassays, such as ELISA assays, immunocytochemistry assays, immunohistochemistry assays, using appropriate clinical samples. The novel monoclonal antibodies and antiserum, obtained from methods of this invention are able to interact and bind HPV viral proteins present in clinical samples, which have been confirmed to contain early stage cell lesions such as cervical intraepithelial neoplasia (CIN) as well as late stage HPV associated cervical cancer. The monoclonal antibodies and antiserum as described herein provide powerful tools to detect and screen HPV related pathogenesis and cervical cancer development in both early stages and late stages; thus provides an avenue to intervene disease progression and a chance to provide early treatment.

3. HPV Monoclonal Antibody Development:

Recombinant HPV E6, E7 or L1 proteins expressed in E coli was purified, concentrated, and dialyzed with PBS to be used as immunogen. Immunization of mice was followed by standard procedure. Titer of the obtained serum was tested by ELISA followed by periodical boosting and bleeding. When the titer of the serum of the mice reaches optimal, fusion of the spleen cells of the mice with tumor cells was done by standard procedure. Clones of fused cells, e.g., hybridoma cells, were further cultured.

1). Hybridoma screening: To obtain anti-HPV antibody producing hybridoma cells with pan and specific binding capability to various HPV proteins as described in this invention, hybridoma clones were screened with various proteins, including, not only the original immunogens but also additional HPV proteins as positive screening, and unrelated proteins as negative screening. For example, two or more purified HPV recombinant proteins were used to screen against each hybridoma clone to screen and obtain monoclonal antibody-producing hybridoma cell lines and to test and understand the specificity of each antibody-producing hybridoma cell line thus obtained.

As an example of hybridoma screening, antibody-producing hybridoma cells were screened with two or more purified recombinant human papillomavirus proteins such that the monoclonal antibody is capable of reacting with the two or more purified recombinant human papillomavirus proteins. The two or more purified recombinant human papillomavirus proteins include, but are not limited to, HPV 16 E6 protein, HPV 16 E7 protein, HPV 16 L1 protein, HPV 18 E6 protein, HPV18 E7 protein, HPV 18 L1 protein, and other HPV early proteins and late proteins from various HPV types.

The antibody-producing hybridoma cells were screened with positive reactivity to all of the two or more purified recombinant human papillomavirus proteins and negative reactivity to non-HPV proteins, including BSA, his₆ tags, GST proteins, maltose binding proteins (MBP), other tags or proteins used in recombinant protein, and other readily available non-HPV proteins. As such, the monoclonal antibodies generated form such hybridoma screening is capable of binding to all of the two or more HPV viral proteins (e.g., the HPV viral proteins present in clinical samples), which correspond to the two or more purified recombinant human papillomavirus proteins.

One example of the two or more purified recombinant human papillomavirus proteins are HPV early proteins such that the monoclonal antibody is capable of reacting with the two or more human papillomavirus early proteins. For example, one hybridoma cell line thus screened and obtained can produce a monoclonal antibody recognizing a common epitope on both HPV16 E6 and HPV16 E7 proteins. Another hybridoma cell line thus screened and obtained can produce a monoclonal antibody recognizing a common epitope on both HPV18 E6 and HPV18 E7 proteins.

Another example of the two or more purified recombinant human papillomavirus proteins includes a purified recombinant human papillomavirus early protein and a purified recombinant human papillomavirus late protein such that the monoclonal antibody produced is capable of reacting with a common epitope on the purified recombinant human papillomavirus early protein and the purified recombinant human papillomavirus late protein. The purified recombinant human papillomavirus early protein may be HPV 16 E6 protein, HPV 16 E7 protein, HPV 18 E6 protein, HPV18 E7 protein, and other HPV recombinant early proteins, and the purified recombinant human papillomavirus late protein may be HPV 16 L1 protein, HPV 18 L1 protein, and other HPV recombinant late proteins. For examples, hybridoma cell lines thus screened and obtained can produce a monoclonal antibody recognizing a common epitope on HPV16 E6, HPV16 E7, and HPV16 L1 proteins; or a monoclonal antibody recognizing a common epitope on HPV16 E6 and HPV18 E6 proteins; or monoclonal antibody recognizing a common epitope on HPV16 E7 and HPV18 E7 proteins; or monoclonal antibody recognizing a common epitope on HPV16 E6, HPV16 E7, HPV16 L1, HPV18 E6, and HPV18 E7 proteins. More examples are provided in the drawings of this invention.

The antibody-producing hybridoma cells were also screened with a first purified recombinant human papillomavirus protein from a first HPV type and a second purified recombinant human papillomavirus protein from a second HPV type such that the monoclonal antibody is capable of reacting with a common epitope on human papillomavirus proteins from two or more different HPV types. The first and the second HPV types can be HPV 16, HPV 18, and other HPV types. The two or more different HPV types can be, for example, high risk HPV types, low risk HPV types, HPV-16, HPV-18, HPV-31, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51, HPV-52, HPV-56, HPV-58, HPV-59, and HPV-68, HPV-6, HPV-11, HPV-42, HPV-43, HPV-44, HPV-53, HPV-54, HPV-55, and HPV-56. As an example, the first and the second purified recombinant human papillomavirus proteins may be recombinant HPV 16 E6 protein, recombinant HPV 16 E7 protein, recombinant HPV 16 L1 protein, recombinant HPV 18 E6 protein, recombinant HPV18 E7 protein, and recombinant HPV 18 L1 protein.

As another example of hybridoma screening, antibody-producing hybridoma cells were screened with positive reactivity to some of the two or more purified recombinant human papillomavirus proteins and negative reactivity to some of the two or more recombinant human papillomavirus proteins and/or non-HPV proteins. As such, the monoclonal antibodies generated form such hybridoma screening is capable of binding to some HPV viral proteins but not other HPV viral proteins.

For example, a monoclonal antibody is obtained by screening antibody-producing hybridoma cells with a first purified recombinant human papillomavirus protein from a first HPV type and a second purified recombinant human papillomavirus protein from a second HPV type such that the monoclonal antibody is capable of reacting with a specific epitope on only one of the first and the second purified recombinant human papillomavirus proteins and not the other purified recombinant human papillomavirus protein. Specific monoclonal antibodies obtained includes a monoclonal antibody capable of binding to only HPV 16 E6 protein, but not any other HPV proteins; a monoclonal antibody capable of binding to only HPV 16 E7 protein, but not any other HPV proteins; a monoclonal antibody capable of binding to only HPV 16 L1 protein, but not any other HPV proteins; a monoclonal antibody capable of binding to only HPV 18 E6 protein, but not any other HPV proteins; and a monoclonal antibody capable of binding to only HPV 18 E7 protein, but not any other HPV proteins.

2). Hybridoma cell line stocks: Hybridoma cell line clones with desired positive reactivity and desired negative reactivity as judged by an immunosays (e.g., ELISA, EIA and other assays) were selected and cloned down to single cell. Each single cell clone was then grown up by tissue culture. When the cell numbers reach millions of cells per ml, the cells were frozen down and kept at −80° C. or in liquid nitrogen as storage stocks.

3). Ascites production: Each hybridoma cell line was grown in tissue culture and injected to mice for ascites production. Ascites were collected and processed for immunoglobin purification by protein G columns. Purified immunoglobin from each hybridoma cell line was isotyped and used for HPV immunoassays.

4. The HPV Immunocytochemical (ICC) Assays:

Sample preparation: Clinical cervical samples can be prepared to be ready for performing the ICC immunoassay by a conventional pap smear sample-obtaining technique which collects cervical cells from cervical scrape and directly smear on one or more slides. Alternatively, a cytology sample-preparation technique which collect cervical sample in a liquid based solution can be used for sample preparation. These cervical scrapes or cervical cells in the liquid based solution were divided into two parts, one for cytological papanicolaou staining, the other for immunocytochemical staining using the various anti-HPV antibodies as described herein.

For Pap smears, each sample was scored from 0-17 after papanicolaou staining: a score of one (1) to three (3) is considered as normal, and four (4) and above as abnormal. The abnormal cells include different stage of squamous cells in development of dysplasia or lesions. For examples, LSIL: Low grade of Squamous Intraepithelial Lesion; HSIL: High grade of Squamous Intraepithelial Lesion; CIN 1: Cervical Intraepithelial Neoplasia; mild cell abnormalities; CIN2: Cervical Intraepithelial Neoplasia with lesions appearing more aggressive; CIN3: Cervical Intraepithelial Neoplasia with aggressive form of dysplasia. Invasive cancers may include squamous cell carcinoma (SCC) adenocarcinoma (ADC), and others. For samples with abnormal cells that can not be determined, they may be scored as ASCUS: Atypical Squamous Cells of Undetermined Significance, unusual or atypical cells in pap smear, may be inconsequential, and the significance of these cells is underdetermined; AGUS: Atypical Glands of Undetermined Significance. For these abnormal cells identified by pap smear scores, further ICC assays by staining with anti-HPV antibodies may provide additional information for the status of HPV infection, cell lesions stages, disease progression, and/or confirm the expression of HPV oncoproteins. Therefore, ICC staining assay with anti-HPV antibody is very useful to detect abnormal cells at either LSIL or HSIL lesion stages, and/or those underdetermined abnormal cells (e.g., ASCUS, or AGUS). The results of ICC immunoassays can also be compared to the scores of the papanicolaou staining.

As an example of an ICC immunoassay, cells from cervical scrapes were directly smeared on the slides for immunostaining. As another example, cervical cells are collected into a liquid based solution, centrifuged, washed, followed by immunostained with anti-HPV antibody. Cervical scrapes collected by Liquid based solution were processed according to manufacture's instruction. The cervical cells were then processed by cytospin or thin prep techniques into a monolayer on a slide.

The thin layer of cells on the slide were then fixed and stained by the various anti-HPV antibodies of the invention. The anti-HPV antibodies may be tagged directly with a detection agent or may be detected by a secondary antibody tagged with a detection agent. Cells stained by the anti-HPV antibody are visualized under microscope.

In one embodiment, a kit for performing an ICC assay is provided. The kit may include an pre-antibody blocking solution, post-antibody blocking solution, an anti-HPV antibody as the primary antibody, an anti-mouse or anti-rabbit immunoglobulins conjugated with HRP or biotin, or other agents as secondary antibody, a solution containing appropriate agents used as substrate for the secondary antibody to be detected.

The anti-HPV antibodies may also be directly tagged with HRP or biotin, or other agents to be detected following appropriate agents used as substrate. The pre-antibody blocking solution may contain certain proteins or BSA, or serum or other agents to block the cells from nonspecific binding of antibody. The post blocking solution may contain similar solution as the pre-antibody blocking solution with less proteins or serum to be used along with primary antibody incubation. The solution containing HPV antibodies may be in concentrated form, or may be in diluted form as ready to use reagent. The solution containing secondary antibodies may be in concentrated form, or may be in diluted form as ready to use reagent. The solution containing appropriate agents used as substrate may include DAB (3.3′-diaminobenzidine) as one component, or two components, or AEC (3-Amino-9-Ethylcarbazole) substrate as one component, or two components, or other substrates.

Once the human cells from cervical scrapes are processed and fixed into a monolayer or thin layer of cells on the slide, the Immunocytochemistry (ICC) assay is performed by blocking the slides with pre-antibody blocking solution for a period of time prior to incubate with the HPV antibodies. The slides were then washed 3 to 5 times with PBS or H20, or other solution to get rid of any unbound HPV antibody. Then the slides were incubated with the secondary antibody, for example, anti-mouse IgG HRP, followed by appropriate substrate for detection. As an example, DAB is oxidized in the presence of peroxidase and hydrogen peroxide resulting in the deposition of a brown, alcohol-insoluble precipitate at the site of enzymatic activity. The precipitate may range in color from a light golden brown to dark golden brown depending upon the amount of enzyme present. The golden brown precipitate viewed under a microscope indicates the specific binding of HPV antibodies with HPV proteins present in the cells. The assay can be performed at room temperature or higher temperature to accelerate the binding reaction. This HPV ICC assay can be performed manually, or operated by ICC automation, thus provides a powerful tool to screen for HPV infection and detection of HPV oncoproteins in situ localized in the epithelium cells from cervical scrapes.

To demonstrate the HPV ICC assay can be applied to different stage of dysplasia cells, samples from early, intermediate, or late stage of neoplasia are all tested. These samples include but not limited to, for example, early stage like LSIL, or CIN1, or ASCUS, or intermediate stage like CIN2, CIN3, or HSIL, or late sage like SCC or ADE or others. To demonstrate the ICC assay described herein can be used to stain for various sample source, or from various stage in various liquid based solution, different stage of samples in different liquid based solution were also prepared to perform ICC assay in this invention.

To demonstrate HPV ICC assays are useful to identify abnormal cells underdetermined by standard cytological papanicolaou staining, for example, ASCUS (Atypical Squamous Cells of Undetermined Significance; unusual or atypical cells in pap smear, may be inconsequential and significance is underdetermined) or AGUS (Atypical Glands of Undetermined Significance), the HPV ICC assays are performed to test ASCUS samples. As shown in FIG. 1A, the results of ICC assay demonstrate that certain cervical scrape cells diagnosed as ASCUS by papanicolaou staining can be ICC stained positively using an anti-E6 monoclonal antibody. FIG. 1B shows the results of ICC assay from the same sample shown in FIG. 1A to demonstrate certain cervical scrape cells (diagnosed as ASCUS by papanicolaou staining) can be ICC stained positively using an anti-E7 monoclonal antibody. As shown in FIG. 1A and FIG. 1B, the abnormal cell with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively while the normal cells (big, irregular cell shape with small nuclear) stain negatively as indicated by the white arrow. Both FIG. 1A and FIG. 1B demonstrate HPV E6 and HPV E7 proteins can be detected in the abnormal cells from sample with pap smear ASCUS. These results indicate that this ASCUS sample containing HPV infected cells with E6 and E7 oncogenic proteins expressed, thus can be detected in situ using the mouse monoclonal anti-HPV E6 and the mouse anti-HPV E7 monoclonal antibody respectively, by the ICC assay described in this invention.

To demonstrate the HPV ICC assay can detect HSIL cells, FIG. 2A shows cervical scrape cells diagnosed as CIN2 by papanicolaou staining prepared in another liquid base solutions can be ICC stained positively using an anti-E7 monoclonal antibody. As shown in FIG. 2A, the CIN2, HSIL abnormal cells in the form of connecting each other with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively to the nucleus and cytoplasm. These results demonstrate that HPV E7 protein present in situ can be detected in the abnormal cells from intermediate stage of neoplasm, in various source of liquid based solution using the mouse monoclonal anti-HPV E7 described here in the ICC assay.

As an another example, FIG. 2B shows another CIN2 sample of cervical scrape cells prepared in another liquid base solutions can be ICC stained positively using an anti-E6 monoclonal antibody. As shown in FIG. 2B, the CIN2, HSIL abnormal cells in the form of connecting each other with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively to the nucleus and cytoplasm. These results demonstrate that HPV E6 protein present in situ can be detected in the abnormal cells from intermediate stage of neoplasm, in various source of liquid based solution using the mouse monoclonal anti-HPV E6 described here in the ICC assay.

To demonstrate the ICC assay described herein can identify intermediate to late stages of cervical intraneoplasm (CIN) cells in liquid based solution, CIN3 cervical scrape samples in different liquid based solution were also prepared to perform ICC assay described in this invention. FIG. 3A shows certain cervical scrape cells (diagnosed as CIN3 by papanicolaou staining) can be ICC stained positively using an anti-E6 monoclonal antibody. FIG. 3B-3D shows another CIN3 using the same anti-HPV E6 mouse monoclonal antibody. As Figures shown, the CIN3, HSIL abnormal cells in the form of connecting each other with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively to the nucleus and cytoplasm. These results demonstrate that HPV E6 protein can be detected in situ in the abnormal cells from intermediate/late stage of neoplasm, in various source of liquid based solution using the mouse monoclonal anti-HPV E6 described here in the ICC assay. These results demonstrate that HPV E6 protein present in situ can be detected in the abnormal cells from CIN3 of liquid based solution using the mouse monoclonal anti-HPV E6 described here in the ICC assay.

FIG. 3E shows the results of of ICC staining from the same CIN3 sample shown in FIG. 3B using an anti-HPV E7 mouse monoclonal antibody. FIG. 3F shows another ICC staining image of the same CIN3 tissue as used in FIG. 3E using the same anti-HPV E7 mouse monoclonal antibody. As shown in the CIN3 lesions of FIGS. 3A-3F, HSIL abnormal cells in the form of connecting each other with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively to the nucleus and cytoplasm. These results demonstrate that HPV E7 protein present in situ can be detected in the abnormal cells from intermediate stage of neoplasm, in various source of liquid based solution using the mouse monoclonal anti-HPV E7 described here in the ICC assay. These results demonstrate that HPV E7 protein present in situ can be detected in the abnormal cells of CIN3 from liquid based solution using the mouse monoclonal anti-HPV E7 described here in the ICC assay.

To confirm p16 is also overexpressed in the late stage of neoplasm, the same CIN3 samples was used to do ICC staining using an anti-p16 mouse monoclonal antibody. FIG. 3G shows the results of ICC staining from the same CIN3 sample shown in FIG. 3B-3F using an anti-p16 mouse monoclonal antibody. As Figures shown, the CIN3, HSIL abnormal cells in the form of connecting each other with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively to the nucleus and cytoplasm. These results demonstrate that p16 protein present in situ can be detected in the abnormal cells from intermediate to late stage of neoplasm. These results demonstrate that HPV E6, HPV E7, and p16 protein present in situ can be detected in the abnormal cells from CIN3 of liquid based solution using the mouse monoclonal antibodies described here in the ICC assay.

As another example to demonstrate the ICC assay described herein can be applied to detect cervical cancer cells in liquid based solution, different carcinoma of cervical scrape samples in different liquid based solution were also prepared to perform ICC assay described in this invention. FIG. 4 shows cervical cancer cells (diagnosed as adenocarcinoma by papanicolaou staining) can be ICC stained positively using an anti-E6 monoclonal antibody. In FIG. 4, the abnormal cell with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively. HSIL abnormal cells in the form of connecting each other were also stained positively. These results demonstrate that HPV E6 protein present in situ can be detected in adenocarcinoma cervical cells in liquid based solution using the mouse monoclonal anti-HPV E6 described here in the ICC assay.

To demonstrate the ICC assay described herein can also be applied to detect another type of cervical cancer cells in liquid based solution, FIG. 5A shows another type of cervical cancer cells, SCC (diagnosed as squamous cell carcinoma by papanicolaou staining) can be ICC stained positively using an anti-E6 monoclonal antibody. FIG. 5B shows the results of ICC staining of the same SCC sample using an anti-HPV E7 mouse monoclonal antibody. FIG. 5C shows the results of ICC staining of the same SCC sample using an anti-p16 mouse monoclonal antibody. As Figures shown, the HSIL SCC cells was stained positively to the nucleus and cytoplasm. These results demonstrate that HPV E6 and HPV E7 protein present in situ can be detected from various type of cervical cancer cells in liquid based solution using the mouse monoclonal anti-HPV E6 or anti-HPV E7 antibodies described here in the ICC assay. To confirm p16 is also overexpressed in the late stage of neoplasm, the same SCC sample was used to do ICC staining using an anti-p16 mouse monoclonal antibody. FIG. 5C shows the results of ICC staining of the same SCC sample shown in FIG. 5A-5B using an anti-p16 mouse monoclonal antibody, indicating that p16 protein present in situ can be detected in the late stage of neoplasm. These results demonstrate that HPV E6, HPV E7, and p16 protein can be detected in situ in the abnormal cells from different type of cervical cancers of liquid based solution using the mouse monoclonal antibodies described here in the ICC assay.

To confirm the ICC staining results described herein are specific binding of the HPV antibody with the HPV proteins present in situ of the cervical scrape cells, normal cervical cells from liquid based solution were also obtained to test on the ICC assay. FIG. 6A shows all cervical scrape cells (diagnosed as normal by papanicolaou staining) prepared in liquid base solutions stained negatively by ICC using an anti-E6 monoclonal antibody. The same samples were also stained by ICC using an anti-HPV E7 monoclonal antibody as shown in FIG. 6B. These results demonstrate that neither HPV E6 protein, nor HPV E7 protein present in situ from the normal cervical scrape cells, thus the ICC assay shows negative staining results using the mouse monoclonal anti-HPV E6 or the mouse monoclonal anti-HPV E7 antibody. Therefore, the results indicate that the ICC assay described in this invention is specific staining method for detection of HPV proteins using the HPV specific antibodies described herein.

In addition, pap smear normal samples were also tested by ICC and found staining negatively (32 out of 32) using anti-HPV antibody. Among the 32 samples, 12 samples were stained with anti-HPV E6 antibody, 16 samples were stained with anti HPV E7 antibody, and 4 samples were stained with anti-HPV L1 antibody. These data indicate that the ICC staining assay described in this invention is very specific. Comparing to HPV DNA test results on the same samples, 19% (6 out of 32) of the pap smear normal samples show positively on HPV DNA test. The high-grade HPV DNA test used in this study was hc2, the only FDA approved HPV DNA test. For those HPV DNA positive but pap smear normal and HPV ICC negative samples, it is possible false positive of the HPV DNA assay, or the DNA detection of HPV infection with no expression of HPV oncogenic proteins. Therefore, the HPV ICC assay described herein provides better clinical relevance for screening of cervical cancer compared to HPV DNA test.

To demonstrate the ICC staining at cellular level, FIG. 7A shows cytoplasmic staining of cervical scrape cells from liquid based solution using a mouse monoclonal Anti-HPV-E6 antibody. FIG. 7B shows nuclear staining of the same sample from FIG. 7A staining by a mouse monoclonal anti-HPV-E7. FIG. 7C shows representative images of cytoplasmic staining from another sample using a mouse monoclonal anti-HPV-E7 antibody. As shown in the figures, the abnormal cell with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively while the normal cells (big, irregular cell shape with small nuclear) stain negatively as indicated by the white arrow. These results indicate that HPV E6 and HPV E7 proteins can be detected in cytoplasm and/or nuclear using the mouse monoclonal anti-HPV E6 and the mouse monoclonal anti-HPV E7 antibody described herein.

To demonstrate HPV E6 E7 oncoproteins can be expressed in certain LSIL (Low grade of Squamous Intraepithelial Lesion) or CIN 1 (Cervical Intraepithelial Neoplasia, mild cell abnormalities), FIG. 8A-8C shows the results of ICC staining of a clinical sample diagnosed as CIN1 in a liquid based solution using an anti-HPV E6 mouse monoclonal antibody. FIG. 8B-8C shows another image of the same ICC staining results shown in FIG. 8A using the same anti-HPV E6 mouse monoclonal antibody. FIG. 8D shows the results of of ICC staining from the same CIN1 sample shown in FIG. 8A using an anti-HPV E7 mouse monoclonal antibody. FIG. 8E shows another image of the same ICC staining results shown in FIG. 8D using the same anti-HPV E7 mouse monoclonal antibody. As Figures shown, the abnormal, LSIL, CIN1 cells in the form of connecting each other or with high N/C (nuclear/cytoplasm) ratio (indicated as black arrow) was stained positively to the nucleus and cytoplasm. These results demonstrate that HPV E6 and HPV E7 protein present in situ can be detected in early stage of neoplasia in liquid based solution using the mouse monoclonal anti-HPV E6 or anti-HPV E7 antibodies described here in the ICC assay. To confirm if p16 is expressed in the early stage of neoplasia, the same CIN1 sample was used to do ICC staining using an anti-p16 mouse monoclonal antibody. FIG. 8F shows the results of ICC staining from the same CIN1 sample shown in FIG. 8A-8E using an anti-p16 mouse monoclonal antibody, indicating that p16 protein can not be detected in the early neoplasia of this CIN1 sample. These results demonstrate that HPV E6, HPV E7 proteins present in situ can be detected in the abnormal cells from early stage of neoplasia using the mouse anti-HPV E6, or anti-HPV E7 monoclaonal antibodies described in this invention, but p16 is not detectable by the anti-p16 mouse monoclonal antibody using the ICC assay described herein.

An immunocytochemical (ICC) assay not only detects HPV infection, but also detects HPV oncogenic proteins in situ. Therefore, ICC assay alone, or in combination with various specific and common anti-HPV antibodies can be a powerful tool for HPV detection in situ, as compared to a standard HPV DNA test or pap smear assay.

TABLE 1 ICC staining results using a mouse anti-HPVE6 monoclonal antibody on various cervical scrape samples in a liquid based solution. Pap smear normal ASCUS ASC-H CIN1 CIN2/3 SCC ICC positive, using  4 3 4 11 17 4 an anti-HPV E6 antibody ICC negative, using 25 6 4  6  0 1 an anti-HPV E6 antibody total 29 9 8 17 17 5 positive rate 14% 33% 38% 65% 100% 80%

Table 1 shows the results of an ICC assay using a mouse anti-HPVE6 monoclonal antibody on various cervical scrape samples in a liquid based solution. The results in Table 1 demonstrate that HPV E6 protein can be detected in situ on single cells fixed on a slide by immunocytochimical (ICC) assay using a mouse monoclonal anti-HPV E6 antibody. The in situ presence of HPV E6 proteins can be detected from various stages of cervical scrape samples in various liquid based solutions. The same cervical scrape samples were also processed by standard papinouli staining to compare the ICC staining results with the pap smear results. As shown in Table 1, HPV E6 proteins are present in the cervical scrape normal, ASCUS, ASC-H, CIN1, CIN2/3 samples with increasing positivity rate, respectively.

There is about 100% positive rate for samples diagnosed with pap smear CIN2/3, while only 14% of samples diagnosed with pap smear normal stained positively by ICC using the same anti-HPVE6 antibody. For ASCUS or ASC-H samples, about 33% to 50% of these samples are stained positively by the same anti-HPV E6 antibody as used for the CIN1, CIN2/3 samples shown in Table 1, indicating expression of oncogenic proteins in these ASCUS or ASC-H sample subjects to be followed up for further cancer progression. For samples with pap smear diagnosed as ASCUS and ICC staining (anti-HPV E6) as negative, it may have less risk to develop progressive lesion.

TABLE 2 Summary of the ICC staining results using a mouse monoclonal anti-HPVE6 antibody on CIN2+ cervical scrape samples in a liquid based solution. Pap smear normal CIN2+ ICC positive, using an 4 21 84% PPV anti-HPV E6 antibody ICC negative, using an 25 1 96% NPV anti-HPV E6 antibody Sensitivity 95% specificity 86%

Table 2 shows summary of the ICC staining results from Table 1. As data indicated, the ICC staining method using the anti-HPV E6 antibody described in this invention provides ICC assay sensitivity of 95% for CIN2+ with specificity of 83%. These data suggest this assay can be useful to detect HPV proteins for screening of cervical cancer from general population along with routine pap smear staining.

TABLE 3 ICC staining results using a mouse monoclonal anti-HPVE7 antibody on various cervical scrape samples in a liquid based solution. Pap smear normal ASCUS ASC-H CIN1 CIN2/3 SCC ICC positive, using  3 4 3 11 16 4 an anti-HPV E7 antibody ICC negative, using 25 6 5  6  1 1 an anti-HPV E7 antibody total 28 10 8 17 17 5 positive rate 11% 40% 38% 65% 94% 80%

As another example of the HPV detecting ICC assay, Table 3 and Table 4 show results of ICC staining using anti-HPV E7 antibody. As data shown, HPV anti-E7 gives comparable ICC results as HPV anti-E6 shown. Table 3 shows that HPV E7 proteins are present in the cervical scrape normal, ASCUS, ASC-H, CIN1, CIN2/3 samples with increasing positivity rate, respectively. There is about 94% positive rate for samples diagnosed with pap smear CIN2/3, while only 11% of samples diagnosed with pap smear normal stained positively by ICC using the same anti-HPVE7 antibody. For ASCUS or ASC-H samples, about 40% of these samples are stained positively by the same anti-HPV E7 antibody as used for the CIN1, CIN2/3 samples shown in Table 3, indicating expression of oncogenic proteins in these ASCUS or ASC-H sample subjects to be followed up for further cancer progression. For samples with pap smear diagnosed as ASCUS and ICC staining (anti-HPV E7) as negative, it may have less risk to develop progressive lesion.

Table 4 shows summary of the ICC staining results from Table 3. As data indicated, the ICC staining method using the anti-HPV E7 antibody described in this invention provides ICC assay sensitivity of 91% for CIN2+ with specificity of 89%. These data suggest this assay can be useful to detect HPV proteins for screening of cervical cancer from general population along with routine pap smear staining.

TABLE 4 Summary of the ICC staining results using a mouse monoclonal anti-HPVE7 antibody on CIN2+ cervical scrape samples in a liquid based solution. Pap Smear Normal CIN2+ ICC positive, using an 3 20 87% PPV anti-HPV E7 antibody ICC positive, using an 25 2 93% NPV anti-HPV E7 antibody Sensitivity 91% specificity 89%

TABLE 5 ICC staining results for pap smear normal samples using various anti-HPV antibodies compared to HPV DNA test Pap smear normal ICC HPV ICC HPV positive negative high-grade HPV DNA 0 6 positive high-grade HPV DNA 0 26 negative

To test if the HPV ICC assay described in this invention is suitable for early stage of cervical cancer screening, pap smear normal samples are used to compare the HPV ICC assay with HPV DNA test. As data shown in Table 5, all pap smear normal samples tested (32 out of 32) stain negatively using anti-HPV antibody. Among the 32 samples, 12 samples were stained with anti-HPV E6 antibody, 16 samples were stained with anti HPV E7 antibody, and 4 samples were stained with anti-HPV L1 antibody. These data indicate that the ICC staining assay described in this invention is very specific. Comparing to HPV DNA test results on the same samples, 19% (6 out of 32) of the pap smear normal samples show positively on HPV DNA test. The high-grade HPV DNA test used in this study was hc2, the only FDA approved HPV DNA test. For those HPV DNA positive but pap smear normal and HPV ICC negative samples, it is possible false positive of the HPV DNA assay, or the DNA detection of HPV infection with no expression of HPV oncogenic proteins. These data indicate that HPV ICC assay described herein provides better positive predictive value compared to HPV DNA test. Thus, the HPV ICC assay provides better clinical relevance for screening of cervical cancer.

5. HPV Flow Cytometry Assay

As another example of immunoassay for detection of HPV proteins, HPV flow cytometry assay is performed. Cells from cervical scrapes collected in liquid based solution following manufacture guideline were centrifuged, washed. Immunostained following the similar ICC staining procedure. Instead of applying cells onto a slide, the cells are kept in solution from staining through analysis by flow cytometry. To perform HPV flow assays, the cervical cells in solution were fixed, blocked and incubated with anti-HPV antibodies followed by appropriate secondary antibody and substrate agents used for detection by flow cytometry. The advantage of this HPV flow cytometry assay is high throughput with no requirement for a highly trained cytologist to view the slides.

In one embodiment, a kit for performing an ICC flow cytometry assay is provided. The kit may include a pre-antibody blocking solution, post-antibody blocking solution, an anti-HPV antibody as the primary antibody, an anti-mouse or anti-rabbit immunoglobulins conjugated with flourecent or biotin, or other agents as secondary antibody, a solution containing appropriate agents used as substrate for the secondary antibody to be detected by flow cytometry.

As an example, indirect labelling requires two incubation steps; the first with a primary antibody followed by a compatible secondary antibody. The secondary antibodies have the fluorescent dye (FITC, PE, Cy5, etc.) conjugated. The anti-HPV antibodies may also be directly tagged with fluorescent, or biotin, or other agents to be detected following appropriate agents used as substrate. The pre-antibody blocking solution may contain certain proteins or BSA, or serum or other agents to block the cells from nonspecific binding of antibody. The post blocking solution may contain similar solution as the pre-antibody blocking solution with less proteins or serum to be used along with primary antibody incubation. The solution containing HPV antibodies may be in concentrated form, or may be in diluted form as ready to use reagent. The solution containing secondary antibodies may be in concentrated form, or may be in diluted form as ready to use reagent.

As an example, the HPV E6, E7, or L1 protein can be detected by the specific antibody followed by the 2^(nd) antibody labeled with fluorescent dye (FITC, PE, Cy5, etc. conjugated). The cells analyzed by flow cytometry can be gated by size or other parameter to look at the cell population with or without staining. The stain intensity from cell population with smaller cell size can be compared to the cell population with bigger cell size as control of normal cells in the assay. This assay provides specific staining for individual cells. Number of cells stained or unstained can be counted, and the intensity of staining can also be quantitated by analysis. This assay can be high throughput, requires no microscope, nor cytologist to score the staining results. The powerful computer software from the flow cytometry provides all data for analysis with no bias or trained personel in cytology required. This assay should apply well in the clinical setting as screening test or accompanion test for detection of HPV associated proteins.

As another example, after the cells are stained, it is better to store the cell suspension immediately at 4° C. in the dark and analyze the cells on the flow cytometer as soon as possible. If longer than an hour before flow analysis, it's necessary to fix the cells. This can preserve them for at least several days. This will stabilize the light scatter and inactivate most biohazardous agents. The fixation for different antigens will require optimization for different assays. Format 1. Paraformaldehyde 0.01% to 1% for 10-15 minutes only, 100 μl per sample. Format 2: Acetone or methanol: Add 1 ml ice cold acetone to each sample. Mix gently. Place at −20° C. for 5 to 10 minutes. Centrifuge, wash twice in PBS 1% BSA

For intracellular staining, cells can be fixed first to ensure stability of soluble antigens or antigens with short half life. This should retain the target protein in the original cellular location. Detection of intracellular antigens requires a cell permeabilization step prior to staining. Antibodies should be prepared in permeabilisation buffer to ensure the cells remain permeable. When gating on cell populations, the light-scatter profiles of the cells on the flow cytometer will change considerably after permeabilization. Antigens in cytomplasmic organelles and granules will require a fixation and permeabilisation method depending on the antigen. The epitope needs to remain accessible.

Fixation could be critical for the quality of staining assay. There are several methods available for fixation: (1) Formaldeyde followed by detergent: Fixation in 0.01% formaldehyde for 10-15 minutes (this will stabilise proteins), followed by disruption of membrane by detergent. Detergents: Triton or NP-40 (0.1 to 1% in PBS). These will also partially dissolve the nuclear membrane and are therefore very suitable for nuclear antigen staining. It should be noted that loss of cell membrane and cytoplasm will result in decreased light scattering and also in reduced non-specific fluorescence. Tween 20, Saponin, Digitonin and Leucoperm are mild membrane solubilisers. Use at 0.5% in PBS. These give large enough pores for antibodies to go through without dissolving plasma membrane. Suitable for antigens in the cytoplasm or the cytoplasmic face of the plasma membrane. Also suitable for soluble nuclear antigens.(2) Formaldehyde (0.01%) followed by methanol. Methanol followed by detergent. Add 1 ml ice cold methanol to each sample. Mix gently. Place at −20° C. for 10 minutes. Centrifuge, wash twice in PBS 1% BSA. Acetone fixation and permeabilisation: Add 1 ml ice cold acetone to each sample. Mix gently. Place at −20° C. for 5 to 10 minutes. Centrifuge, wash twice in PBS 1% BSA

The one or more immunological assays using antibodies and purified recombinants proteins derived from HPV early and/or late genes as obtained herein serve as reliable indicators whether HPV infection has occurred. In addition, HPV associated malignancy or pre-malignant cell transformation can be assayed. One of the most useful aspects of the invention is in diagnosing cervical carcinoma, both squamous cell carcinoma and adenocarcinoma as well as any epithelial cell abnormality associated with oncogenic HPV infection including koilocytosis; hyperkerotosis; precancerous conditions encompasssing intraepithelial neoplasias or intraepithelial lesion; high-grade dysplasias; and invasive or malignant cancers.

In one embodiment, the early gene that can be used herein may include papillomavirus E6 genes, papillomavirus E7 genes, among others. In another embodiment, the late gene that can be used herein may include papillomavirus L1 genes, papillomavirus L2 genes, among others.

One aspect of the invention provides recombinant proteins, such as a recombinant hybrid protein containing a full length sequence of HPV oncogenic proteins, e.g., full-length E6, E7, and/or L1 polypeptide sequence, which have been found very difficult to obtain and purify due to undesirable aggregation during protein purification, protein instability, low levels of expression, low immunogenic responses of purified proteins. For example, many early E6 oncoproteins contain many cysteine amino acids and thus the correct topography of the E6 oncoproteins requires formation of many disulfide bonds properly. In addition, it was known that certain immunological assays using small peptides of early E6 and E7 proteins results in extremely low assay specificity and sensitivity and thus unsuitable to commercialize for in vitro diagnostics.

In high grade CIN lesions, E6 and E7 are strongly expressed in host basal epithelial cells and interfere substantially with cell cycle control of these replication competent host cells. Expression of HPV oncoproteins interfers with G1-S-Phase regulation in host cells. The HPV E6 and E7 proteins target a plethora of cellular interactions, such as the inactivation of pRB by E7 and the degradation of p53 by E6. High level of HPV E7 proteins inactivates pRB and leads to disruption of E2F-Rb binding. Usually, binding of pRB to E2F blocks E2F driven cell cycle activation. In replicating cells, E2F is regulated by phosphorylation of RB. Rb phosphorylation is normally mediated by cyclin dependent kinases (CDK4, CDK6) that are controlled by several kinase inhibitors (INKs).

As a result of the loss of Rb/E2F repression and the strong activation by free E2F, the expression of a host cell protein, p16INK4a, is strongly overexpressed. In addition, S-phase genes are continuously activated since the p16INK4a mediated repression of Cdk4/6 has no downstream effect on pRb host cell protein. Since E7-dependent E2F release is not mediated by phosphorylation of pRb, the counter-regulatory p16INK4a expression has no effect on the activated cell cycle. Under physiological conditions p16INK4a is expressed when cells undergo a genomic stress situation such as substantial shortening of telomeres in aging tissues. Also, apoptosis is abrogated by HPV E6 mediated degradation of p53. The overexpression of the cyclin dependent kinase (CDK) inhibitor, p16INK4a, is a direct consequence of deregulated HPV oncogene expression.

In addition, host cell proteins important for proliferation and host cell genome replication may be overexpressed as a result of HPV infection. These host cell proteins include, ki67 (MIB-1), MYC cellular oncogene, Cyclin proteins (e.g., cyclin A, B, E, etc.), CDKN2A/p16INK4a, telomerase (e.g., TERC), replication complex proteins (e.g., MCM5, CDC6, topoisomerase 11 alpha (TOP2A), MCM2, minchromosome maintenance proteins 2, 4, and 5, etc.).

As an example, the immunological assays for detection of HPV proteins, such as E6, E7, L1, etc., or immune response thereof due to HPV infection can be performed in high throughput ELISA screening assays, rapid immunological screening assays, and additional multiplexed protein chip assays, etc., and combinations thereof. Embodiments of the invention provides various polyclonal and monoclonal antibodies for HPV proteins to be used in one or more assays, including an antibody, antigen, or immunocomplex assays developed to detect HPV viral proteins encoded by early genes (e.g., E6 and E7) and late genes (e.g., L1). In addition, the developed antibody, antigen, or immunocomplex assays for E6, E7, L1, protein or their antibodies thereof in one format, for example, a microplate format, can be adapted into a one-step immunochromatographic assay for the direct measurement of E6, E7, L1 proteins or antibodies induced by HPV infection. The one or more immunological assays as provided herein aims to employ user friendly procedures with simple instrument or no additional instrument to perform in a short period of time. Comparison of the results of the various immunological assays, nucleic acid hybridization assays with cytological and histological data for the human subjects as well as demographic information serve to validate the correlation and accuracy in diagnosing HPV infection and/or cervical cancer.

Another example of a method of screening a human subject infected with a human papillomavirus may include obtaining a clinical sample from the human subject, conducting a nucleic acid hybridization assay on the clinical sample, detecting the presence of a papillomavirus genome in the clinical sample from the human subject, conducting one or more immunological assays on the clinical sample, detecting the presence of an antibody to an early papillomavirus viral protein or the presence of the early papillomavirus viral protein in the clinical sample using a first recombinant protein of the early papillomavirus viral protein, and detecting the presence of an antibody to a late papillomavirus viral protein or the presence of the papillomavirus late viral protein in the clinical sample using a second recombinant protein of the late papillomavirus viral protein.

The one or more diagnostic immunological assays as described therein may also include obtaining polyclonal antibodies, monoclonal antibodies, and/or antiserum specific against the one or more recombinant proteins as obtained and described herein, taking a clinical sample likely to contain HPV associated proteins and/or antigens, reacting it with the obtained polyclonal antibodies, monoclonal antibodies, and/or antiserum specific for the one or more recombinant proteins, and assaying for the presence of any antibody-antigen complexes by suitable detection systems. Suitable detection system may employ various colormetric, chemilumenescent, flourescent substrates, etc., specific for a secondary antibody used in each immunological assay.

Early diagnosis of HPV infection is important for successful prevention and treatment of cervical cancer. Strategies to prevent cervical cancer requires improved HPV testing/screening to cover a broad range of the worldwide population in addition to closely follow-up those subjects with past or present HPV infection and/or pre-cancerous lesions. Importantly, it is known that infection in women for 12-15 years with HPV is required before invasive cancer to develop. It is thus important to be able to assay biomarkers for HPV infection as described herein to pre-screen women early, such that it will be possible to treat HPV infection early and prevent cervical cancer development, rather than having to rely on chemotherapy or radiation to treat cancer malignancy. 

1. A method of detecting papillomavirus infection in a human subject, comprising: providing a clinical sample from the human subject, the clinical sample containing a mixture of morphologically abnormal and normal human cells are processed and applied into a thin layer of cells on a slide; conducting an immunocytochemistry assay using one or more antibodies generated against one or more purified recombinant papillomavirus proteins, wherein at least one antibody is capable of binding to a papillomavirus early viral protein; and staining in situ one or more papillomavirus viral proteins from one or more papillomavirus types present in the clinical sample on the slide containing the mixture of morphologically abnormal and normal human cells.
 2. The method of claim 1, wherein the one or more purified recombinant papillomavirus proteins are selected from the group consisting of recombinant HPV-16 E6 proteins, recombinant HPV-16 E7 proteins, recombinant HPV-18 E6 proteins, recombinant HPV-18 E7 proteins, recombinant HPV-16 L1 proteins, recombinant HPV-18 L1 proteins combinations thereof.
 3. The method of claim 1, wherein the papillomavirus early viral protein is selected from the group consisting of HPV-16 E6 protein, HPV-16 E7 protein, HPV-18 E6 protein, HPV-18 E7 protein, and combinations thereof.
 4. The method of claim 1, wherein the one or more papillomavirus, viral proteins are selected from the group consisting of papillomavirus E6 protein, papillomavirus E7 protein, papillomavirus L1 protein and combinations thereof.
 5. The method of claim 1, wherein the one or more papillomavirus types are selected from the group consisting of high risk HPV types, low risk HPV types, HPV-16, HPV-18, HPV-31, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51, HPV-52, HPV-56, HPV-58, HPV-59, and HPV-68, HPV-6, HPV-11, HPV-42, HPV-43, HPV-44, HPV-53, HPV-54, HPV-55, and HPV-56, and combinations thereof.
 6. The method of claim 1, wherein one antibody among the one or more antibodies is capable of binding to two or more papillomavirus viral proteins.
 7. The method of claim 6, wherein the two or more papillomavirus viral proteins comprises the papillomavirus early viral protein and a papillomavirus late viral protein and the one antibody is capable of binding to both the papillomavirus early viral protein and the papillomavirus late viral protein.
 8. The method of claim 1, wherein the one or more antibodies are selected from the group consisting of antibodies capable of binding to HPV E6 proteins, antibodies capable of binding to HPV E7 proteins, antibodies capable of binding to HPV E6 and E7 proteins, antibodies capable of binding to HPV L1 proteins, antibodies capable of binding to HPV E6 proteins from different HPV types, antibodies capable of binding to HPV E7 proteins from different HPV types, antibodies capable of binding to HPV L1 proteins from different HPV types, antibodies capable of binding to HPV E6 and E7 proteins of the same HPV types, antibodies capable of binding to HPV E6 and E7 proteins of different HPV types, antibodies capable of binding to HPV E6, E7, and L1 proteins, and combinations thereof.
 9. The method of claim 1, wherein the immunocytochemistry assay is used to detect a diseased stage caused by HPV infection, the disease stage is selected from the group consisting of early stage HPV infection, late stage HPV infection, early stage cervical lesion, late stage cervical lesion, low grade of squamous intraepithelial lesion (LSIL), high grade of squamous intraepithelial lesion (HSIL), atypical squamous cells of undetermined significance (ASCUS), cervical intraneoplasm stage 1, 2, 3 (CIN1, CIN2, CIN3, respectively), invasive cervical cancer, adenocarcinoma (ADC), squamous cell carcinoma (SCC), and combinations thereof.
 10. The method of claim 1, further comprising performing a cytological papanicolaou smear assay on the clinical sample and comparing the results of the cytological papanicolaou smear assay with the results of the immunocytochemistry assays.
 11. The method of claim 1, further comprising comparing the staining pattern and intensities of the mixture of the morphologically abnormal and normal human cells with the morphology of these cells.
 12. The method of claim 1, wherein the staining in situ on the slide the one or more papillomavirus proteins from the one or more papillomavirus types present in the clinical sample comprises under a microscope detecting the presence of an agent tagged on the one or more antibodies, wherein the agent is selected from the group consisting of a colormetric agent, a fluorescent chromogen, and combinations thereof.
 13. The method of claim 1, wherein the conducting the immunocytochemistry assay further comprises using two or more anti-HPV antibodies pre-labeled with different agents in one binding reaction to detect more than one HPV proteins.
 14. The method of claim 1, wherein the clinical sample is selected from the group consisting of cervical cells, cervical tissues, cervical swabs, body fluids, serum, blood, tumors, cell cultures, biopsies, and combination thereof.
 15. The method of claim 1, wherein the clinical sample is obtained from general population and the immunocytochemistry assay is conducted for the detection of cervical cancer.
 16. A method of detecting papillomavirus infection in a human subject, comprising: providing a clinical sample from the human subject, the clinical sample is processed into a liquid-based solution containing a mixture of morphologically abnormal and normal human cells; staining the mixture of the morphologically abnormal and normal human cells using one or more antibodies generated against one or more purified recombinant papillomavirus proteins, wherein the one or more antibodies are each tagged with an agent, and at least one antibody is capable of binding to a papillomavirus early viral protein; conducting one or more flow cytometry assays to detect each individual cells by separating each cell from the mixture of the morphologically abnormal and normal human cells; and detecting the presence of one or more human papillomavirus viral proteins from one or more papillomavirus types in the mixture of the morphologically abnormal and normal human cells contained in the liquid-based solution from the clinical sample.
 17. The method of claim 16, wherein the one or more antibodies further comprises two or more anti-HPV antibodies each pre-labeled with different agents and used in one binding reaction to detect the presence of two or more human papillomavirus viral proteins.
 18. A kit for detecting papillomavirus infection in a human subject, comprising: an anti-HPV monoclonal antibody, capable of binding to a papillomavirus early protein for conducting an immunocytochemistry assay on a clinical sample from the human subject processed into a solution containing a mixture of morphologically abnormal and normal human cells and applied into a thin layer of cells on a slide for staining in situ one or more papillomavirus viral proteins from one or more papillomavirus types present in the clinical sample on the slide containing the mixture of morphologically abnormal and normal human cells.
 19. The kit of claim 18, wherein the anti-HPV antibody is selected from the group consisting of an anti-HPV E7 monoclonal antibody, an anti-HPV E6 monoclonal antibody, a combination of an anti-HPV L1 antibody and anti-HPV E7 monoclonal antibody, a combination of an anti-HPV L1 antibody and anti-HPV E6 monoclonal antibody, a combination of an anti-HPV E6 antibody and anti-HPV E7 monoclonal antibody.
 20. The kit of claim 18, wherein the one or more papillomavirus types are selected from the group consisting of high risk HPV types, low risk HPV types, HPV-16, HPV-18, HPV-31, HPV-33, HPV-35, HPV-39, HPV-45, HPV-51, HPV-52, HPV-56, HPV-58, HPV-59, and HPV-68, HPV-6, HPV-11, HPV-42, HPV-43, HPV-44, HPV-53, HPV-54, HPV-55, and HPV-56, and combinations thereof. 